What is Mcp Server Biorxiv

mcp-server-bioRxiv is a server that enables AI assistants to search and access bioRxiv papers through a simple Model Context Protocol (MCP) interface, acting as a bridge between AI models and bioRxiv’s preprint repository.

Use cases

Use cases include facilitating literature reviews, supporting research projects, enabling AI-driven analysis of biological data, and providing quick access to the latest preprints in the field.

How to use

To use mcp-server-bioRxiv, clone the repository from GitHub, install the required dependencies using pip, and follow the installation instructions for various AI clients like Claude, Cursor, Windsurf, and CLine.

Key features

Key features include paper search with keywords, efficient retrieval of paper metadata, detailed metadata access, support for biological sciences research, paper content download, local storage of papers for faster access, and specialized research prompts for analysis.

Where to use

mcp-server-bioRxiv is primarily used in the field of biological sciences, particularly for researchers and AI assistants who need to access and analyze preprint research papers.

bioRxiv MCP Server

🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface.

The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv’s preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their metadata in a programmatic way.

🤝 Contribute • 📝 Report Bug

✨ Core Features

• 🔎 Paper Search: Query bioRxiv papers with keywords or advanced search ✅
• 🚀 Efficient Retrieval: Fast access to paper metadata ✅
• 📊 Metadata Access: Retrieve detailed metadata for specific papers ✅
• 📊 Research Support: Facilitate biological sciences research and analysis ✅
• 📄 Paper Access: Download and read paper content 📝
• 📋 Paper Listing: View all downloaded papers 📝
• 🗃️ Local Storage: Papers are saved locally for faster access 📝
• 📝 Research Prompts: A set of specialized prompts for paper analysis 📝

🚀 Quick Start

Prerequisites

• Python 3.10+
• FastMCP library

Installation

1. Clone the repository:

   git clone https://github.com/JackKuo666/bioRxiv-MCP-Server.git
   cd bioRxiv-MCP-Server
   

2. Install the required dependencies:

   pip install -r requirements.txt
   

Installing via Smithery

To install bioRxiv Server for Claude Desktop automatically via Smithery:

claude

npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client claude --config "{}"

Cursor

Paste the following into Settings → Cursor Settings → MCP → Add new server:

• Mac/Linux

npx -y @smithery/cli@latest run @JackKuo666/biorxiv-mcp-server --client cursor --config "{}" 

Windsurf

npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client windsurf --config "{}"

CLine

npx -y @smithery/cli@latest install @JackKuo666/biorxiv-mcp-server --client cline --config "{}"

Usage with Claude Desktop

Add this configuration to your claude_desktop_config.json:

(Mac OS)

{
  "mcpServers": {
    "biorxiv": {
      "command": "python",
      "args": [
        "-m",
        "biorxiv-mcp-server"
      ]
    }
  }
}

(Windows version):

{
  "mcpServers": {
    "biorxiv": {
      "command": "C:\\Users\\YOUR_USERNAME\\AppData\\Local\\Programs\\Python\\Python311\\python.exe",
      "args": [
        "-m",
        "biorxiv-mcp-server"
      ]
    }
  }
}

Using with Cline

{
  "mcpServers": {
    "biorxiv": {
      "command": "bash",
      "args": [
        "-c",
        "source /home/YOUR/PATH/mcp-server-bioRxiv/.venv/bin/activate && python /home/YOUR/PATH/mcp-server-bioRxiv/biorxiv_server.py"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": []
    }
  }
}

📊 Usage

Start the MCP server:

python biorxiv_server.py

🛠 MCP Tools

The bioRxiv MCP Server provides the following tools:

1. search_biorxiv_key_words: Search for articles on bioRxiv using keywords.
2. search_biorxiv_advanced: Perform an advanced search for articles on bioRxiv with multiple parameters.
3. get_biorxiv_metadata: Fetch metadata for a bioRxiv article using its DOI.

Searching Papers

You can ask the AI assistant to search for papers using queries like:

Can you search bioRxiv for recent papers about genomics?

Getting Paper Details

Once you have a DOI, you can ask for more details:

Can you show me the metadata for the paper with DOI 10.1101/123456?

📁 Project Structure

• biorxiv_server.py: The main MCP server implementation using FastMCP
• biorxiv_web_search.py: Contains the web scraping logic for searching bioRxiv

🔧 Dependencies

• Python 3.10+
• FastMCP
• asyncio
• logging

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

📄 License

This project is licensed under the MIT License.

⚠️ Disclaimer

This tool is for research purposes only. Please respect bioRxiv’s terms of service and use this tool responsibly.